This is a companion repository for the R package adaptBayes available at https://github.com/umich-biostatistics/adaptBayes. The adaptBayes package
contains the code for actually fitting an adaptive prior in a Bayesian GLM.
This repository only contains the additional code needed for conducting the
simulation study in Boonstra and Barbaro (2018). Before you can use this
repository, you need to first install and load the adaptBayes package using
the following commands:
if(!require(adaptBayes)) {
library(devtools)
# if installation is necessary, compiling everything will take a few minutes
install_github('umich-biostatistics/adaptBayes')
} After installing the package, you can use the scripts in this repository to
reproduce the simulations studies in the manuscript. See also vignette.pdf
for a vignette describing the typical usage of the adaptive Bayesian priors on
a simulated dataset
In more detail, there are six files included in this repository (in addition to
this README and vignette.pdf): one text file (run_abu_sims.txt)
and five R scripts (ending in .R). The simulation
studies reported in Boonstra and Barbaro were run using commit 22
run_abu_sims.txt is the script for submitting parallel runs of run_aub_sims.R (described below) to a cluster that is running SLURM. The following command run in terminal will do this:
sbatch run_abu_sims.txt
The script assumes that you want all of the results to be put in your home directory (which you probably don't). Edit the script as needed
vignette.R creates a single simulated dataset and walks through
analyzing these data using the various adaptive priors. It can also be knit
to create a copy of vignette.pdf (it will take a few minutes to knit)
run_abu_sims.R is the script to conduct the large-scale simulation study described in the manuscript. On a local machine, the user may choose a specific array_id (as described in this script's documentation) and run the code locally on his/her machine. On a cluster running SLURM, the user can use this script to submit multiple jobs simultaneously (as described in the description of run_abu_sims.txt above).
functions_simulation.R provides the simulation functions. NOTE:
this only contains the extra functions needed to simulate the data; the methods
are contained in the adaptBayes package
generate_params.R constructs inputs for running the simulation study. As described in the script's documentation and the language below, these inputs can be overwritten by the user
make_figures.R gives the code to create the figures and tables in the manuscript and supplementary material reporting on the simulation study.
Boonstra, Philip S. and Barbaro, Ryan P., "Incorporating Historical Models with Adaptive Bayesian Updates" (2018) Biostatistics https://doi.org/10.1093/biostatistics/kxy053
DOI for this repository:
